name: "genomescope2"
description: Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach
keywords:
  - "genome size"
  - "genome heterozygosity"
  - "repeat content"
tools:
  - "genomescope2":
      description: "Reference-free profiling of polyploid genomes"
      homepage: "http://qb.cshl.edu/genomescope/genomescope2.0/"
      documentation: "https://github.com/tbenavi1/genomescope2.0/blob/master/README.md"
      tool_dev_url: "https://github.com/tbenavi1/genomescope2.0"
      doi: "https://doi.org/10.1038/s41467-020-14998-3"
      licence: "['Apache License, Version 2.0 (Apache-2.0)']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - histogram:
      type: file
      description: A K-mer histogram file
      pattern: "*.hist"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - linear_plot_png:
      type: file
      description: A genomescope2 linear plot in PNG format
      pattern: "*_linear_plot.png"
  - linear_plot_png:
      type: file
      description: A genomescope2 linear plot in PNG format
      pattern: "*_linear_plot.png"
  - transformed_linear_plot_png:
      type: file
      description: A genomescope2 transformed linear plot in PNG format
      pattern: "*_transformed_linear_plot.png"
  - log_plot_png:
      type: file
      description: A genomescope2 log plot in PNG format
      pattern: "*_log_plot.png"
  - transformed_log_plot_png:
      type: file
      description: A genomescope2 transformed log plot in PNG format
      pattern: "*_transformed_log_plot.png"
  - model:
      type: file
      description: Genomescope2 model fit summary
      pattern: "*_model.txt"
  - summary:
      type: file
      description: Genomescope2 histogram summary
      pattern: "*_summary.txt"

authors:
  - "@mahesh-panchal"